Sepia the Mouse: A Shadow of the Past
by Watership's Nightwish Rat
Summary: Sepia the Mouse is haunted by dreams having to do with her past, which she does not remember. Little does she know, her past is somehow connected to that of Shadow the Hedgehog. As she pieces together the events of her lost life, she finds herself caught in the middle of a war with the villainous scientist, Doctor Eggman...
1. Sepia

**Author's Notes: **

**All characters, except for Sepia the Mouse, are created by Sega. Sepia the Mouse was created by me. That being said, please read and enjoy the story.  
**

* * *

_There were the sounds of explosions and gunfire as Shadow the Hedgehog speedily led his friend Maria through the small hallway of Space Colony ARK, GUN soldiers hot on their heels. They ran into the nearest room, where an escape capsule was prepared. Maria pushed Shadow in and closed it. The perturbed hedgehog banged on the glass capsule fearfully, not willing to leave the young girl behind to die. Maria, however, ignored Shadow's rage as she placed her hands on a lever. A soldier barged in at that moment. "Let go of the lever and surrender!" he ordered. "If you don't, I'll shoot!"_

_Maria was terrified, but she was not about to let him take Shadow. "No!" she shouted anxiously. "Leave my friend alone!"_

_Shadow watched in horror at the events that followed. Just as Maria pulled the lever, the soldier squeezed the trigger of his pistol._

_"Maria!" Shadow cried out in dismay as his friend was struck by the bullet._

_The girl fell to the floor next to the capsule. "Shadow, I need you to do something for me: protect the people on Earth from what is to come. It... all depends on... you!" Maria went still as death overwhelmed what was left of her life._

_Shadow's vision was blinded by his tears. "Maria!" he cried again, just a split second before the capsule shot down to Earth._

_The soldier looked at his gun in disbelief after Shadow unwillingly departed. "Oh no!" he thought in frustration. "What have I done?!"_

_Back in the capsule, the black hedgehog suddenly realized that he was not alone. He heard a small voice sobbing uncontrollably behind him. "Who-who's there?" he stammered in a depressed voice._

_A young, light brown mouse with fluffy black and red head fur stepped forward slowly, tears streaming down her face. "It's j-just me, Sh-Shadow," she choked._

_"Sepia?" Shadow said in disbelief. "I thought you were still in ARK!"_

_**M**_

Sepia the Mouse woke up at that moment. "How long have I been having this nightmare?" she wondered. "Who are Shadow and Maria? What and where is ARK? Why can't I remember anything about those things, or my past for that matter?"

The brown mouse sat up from the green grass she had lay in that night, stroking her long black head fur as she recalled the events she _could_ remember had happened. Sepia had woken up from a slumber of who-knows-how-long just a few days ago in Doctor Eggman's laboratory. She knew that his claims of her being his servant were lies and fought off all of his robots blocking her path on her way out. Since then, she had been laying as low as she could while Eggman's robots kept searching for her relentlessly. She met no one thus far, which made her feel alone in her battle to be out of the doctor's clutches for as long as possible, if not permanently. But she still had high hopes of finding someone who would help her, whether they knew about her past or not.

"I'd rather not know my past than be all alone," she thought, "or be back at that Eggman jerk's place as a slave."

Something inside her told her, not incorrectly, that Eggman knew the truth about her past.

**_M_**

"Come on Shadow, tell me! You're usually quiet and antisocial, but not quite like this!"

That was Rouge the Bat talking. Shadow the Hedgehog had been extremely annoyed and troubled all morning, but Rouge could sense that it was not because of her-well, not _just_ because of her. Even though the bat kept urging him to spill the beans, Shadow stayed silent and simply glared at her.

Rouge suddenly thought of something. "Was it that dream you had about Maria?" she asked calmly.

Shadow closed his eyes in frustration and turned away. "Why do you care?" he hissed. "You didn't even see her before."

"I care because you're my friend," the bat answered, still keeping the calm in her voice. "But it wasn't just Maria in that dream, was it?"

The hedgehog sighed sadly and turned to face his ally. "It wasn't just her, there were also the soldier who killed her, and an old friend of mine who was killed when I was captured on Earth."

Rouge was about to press him to explain about this old friend when they both heard some cries for help. "It's Amy, Tails and Cream!" she exclaimed.

"How many times must we tell them _not_ to wander around by themselves?" Shadow asked himself in frustration.

**_M_**

Sepia also heard the three young creatures call out for help. She knew that Eggman was the cause of their distress, but she did not care: she _had_ to get them to safety, even if it meant being captured in the process. Sepia looked over the hill she was behind and peered at the scene below. A pink hedgehog, a multi-hues of brown rabbit, a blue and yellow chao, and a two-tailed yellow fox were completely surrounded by Eggman himself and his robots.

"There's nowhere for you to run to," Eggman said evilly. "You might as well surrender now."

"No!" Tails shouted. "We will _never_ surrender to you!"

Eggman smiled wickedly. "Is that so? Well, I guess it's time for you to meet your maker!"

"Not on my watch, Fatty!" Sepia shouted as she stood up from where she was.

"You!" Eggman shouted as he looked in Sepia's direction. "I should have known you'd get this far just to make that stupid move you made."

"Look Eggman, if you want to catch me, you'll have to let them go first," the mouse said boldly.

The evil doctor was only a little shocked. He called to his robots to let Amy, Cream and Tails leave before sending them after Sepia. Sepia turned around and darted in the other direction. She was fast, but not nearly as fast as Eggman's robots. A robot grabbed her by her light blue shirt. The mouse struggled before she suddenly disappeared. All of the robots witness were dazed for a moment.

"Up here, punks!" Sepia called from the top of a tall hill. She had no idea how she got there, but she knew it was a power she had that she had not known how to use. Still, she kept her focus on her situation.

**_M_**

Shadow and Rouge literally bumped into Amy, Tails and Cream. "What's the problem?" Shadow demanded to know.

"Eggman had us surrounded!" Amy explained anxiously.

"There was a mouse there who had him let us go!" Tails chimed in.

Cream was close to tears. "She's being chased by Eggman right now!"

Cheese fought back tears of his own. "Chao!" he anxiously agreed with Cream.

Rouge looked at Shadow seriously. "I'll get these three home," she said. "You go and help the girl being chased by Eggman."

"That's what I had in mind," Shadow said curtly. He dashed as fast as he could in the direction he felt was where Eggman was chasing the mouse to.

* * *

**Author's Notes:**

**If you noticed me going out of character with some characters, note that I sometimes have a tough time with that. Also, I don't really know if Cheese is a boy or a girl, so I'm calling Cheese a boy in this story. **

**Please tell me what you think!  
**


	2. Reunion and Sonic's Whereabouts

**Author's Notes:**

**Here's part 2 to the story. Please note that this chapter includes more violence than the previous one, so if you are sensitive to violence and or blood, I advise that you don't read this. There is, however, more humor in this chapter.  
**

**Enjoy...  
**

* * *

"Get her!" Eggman ordered his robots.

Sepia turned her back to the robots and ran again, only to find that her path was cut off by a tall cliff. She could not afford to try to climb up it, for she knew for sure that she was not strong enough to get all the way up there. Before she knew what was going on, the robots were closing in on her. Sepia backed up to the cliff face with her small fists clenched and held just inches away from her chest, ready to fight off as many of her attackers as she could.

Eggman looked at her evilly. "That's kind of cute!" he mocked. "Do you honestly think that you can take _all_ of my robots down?"

The mouse glared at her adversary icily. "No, but I'd rather die trying than be stuck with you!" she stated coldly.

The doctor winced at this remark. "That really hurts! Time to teach you a lesson about disrespecting your maker."

"You're not my maker, Egghead!" Sepia snapped. "I may not know all of my past, but I know for sure that you did not create me!"

Doctor Eggman motioned to his robots. "Attack her, attack!" he ordered.

Sepia was quickly covered by the robots, but she still refused to give in. She kicked off half of them and threw the other half all at once at the cliff face, destroying only one-fourth of them. Those that were not destroyed came at her from behind as the remaining robots tightly encircled her. Sepia acknowledged that she could only fight them all off until they killed her.

"Chaos Spear!"

Half of the remaining robots were suddenly destroyed at the same instant. Sepia was shocked to see the black hedgehog from her dreams appear behind her from seemingly out of nowhere. "Shadow," Sepia thought in amazement.

Shadow looked at Sepia with an uncanny grin on his face. "Ready for this, kid?" he asked competitively.

The mouse nodded, returning the grin as she did so. "Ready as I'll ever be, Shad," she replied.

Eggman could only watch in awe as Shadow and Sepia annihilated his robots in a matter of seconds. Shadow used his Chaos Spear power, which destroyed several of them at a time, as Sepia tripped several robots with her tail while puching and kicking others' machanical heads off, the broken wires sparking as the bodies fell to the ground. Once there were only two enemies left, Shadow grabbed Sepia and thrust her into the air. She held a fist next to her chest before thrusting her arm at the robots and opened her hand, allowing lightning bolts to strike them. She was caught by Shadow during her fall as the robots exploded.

"You two won't be so lucky next time!" Eggman declared. He turned his hovercraft around and headed back to his base.

Sepia watched Eggman flee as Shadow carried her back the way he came. She was about to request being put back down when she realized that there were some pieces of the destroyed robots' metal lodged sharply in her legs. Panic suddenly overcame her senses. Shadow sped his pace to a dash as he felt the mouse's blood run down his arm and soak his white gloves with its red hue. Sepia struggled to regain her calm but failed as her energy drained faster and faster with each second that went by.

"Vanilla!" Shadow shouted urgently. "Get a bed ready, quick!"

A tall rabbit saw Shadow and Sepia's predicament before rushing into her house to one of the guest rooms. Within seconds, she had completed Shadow's request. "In this one, Mister Shadow," she said as quickly and kindly as she could. "There's also a first aid kit next to the bed."

Shadow managed a kind smile, which was very rare of him. "Thanks, Vanilla," he said thankfully to the rabbit.

"You're very welcome," Vanilla kindly said, hiding the fact that she noticed Shadow's change of behavior.

The mouse suddenly calmed down when Shadow laid her gently on the bed, looking into his eyes for the first time in fifty years. Shadow grabbed the first aid kit and opened it. He pulled out some bandages, a couple of thick rubber bands and antibacterial ointment before removing the metal shards from Sepia's legs, which caused her to bleed faster. Shadow tightly wrapped a rubber band around the upper part of each leg. He rubbed some ointment on the wounds before wrapping some of the bandages around and over the legs. After twenty minutes, which seemed like forever to Sepia, Shadow removed the rubber bands. During that time, Sepia tried to pass the time by talking to her long lost friend. The hedgehog, however, remained quiet and serious until he removed the bands.

"Just stay here for a few days, Sepia," he said at last. "Whatever you do, _don't use your legs_."

"But what if I need to use the bathroom?" Sepia asked in terror.

Vanilla walked in at that moment with Cream. "I'll carry you to the bathroom, sweetie," she said in her sweet voice. "And don't worry if you accidently go in my arms: my sweet Cream here did the same exact thing when she was little."

Cream's face burned with embarrassment, but made no comment to her mother. She instead, (with the company of her pet chao Cheese, and her friends Amy and Tails), approached Sepia's bed and kept a few feet away from it. "Thank you for saving us, Miss Sepia," she said sweetly.

Cheese smiled and happily cheered, "Cha-chao chao!"

Sepia grinned heartily. "No problem, Cream. Just try to stay out of trouble from now on."

Shadow shot Sepia a look that told her everything: "She says that, but she never does." He turned to Vanilla. "I gotta go," he stated. "Thanks for your help."

"You're very welcome, Mister Shadow. I'll make sure Miss Sepia recovers correctly."

Just as Shadow turned to leave, Sepia called out, "Shadow, wait a minute!"

The hedgehog looked at her seriously. "What now?" he muttered darkly.

Sepia looked into his eyes calmly. "Thank you," she said gently. Her tone gained a little bit of seriousness. "Do you know of a hedgehog named Sonic?"

Amy, Tails, Vanilla, and Cream gasped in shock. _How did she know about Sonic? She was new here, wasn't she?_ Shadow simply nodded. "Yeah, I know him, but what about him?"

"When I woke up a few days ago, I overheard Doctor Eggman in conversation," Sepia explained. "I think I heard him address whoever he was talking to as Sonic."

Shadow eyed the mouse even more seriously. "Did you happen to hear his voice?" he asked.

"Yes, but only a little bit."

"Was it cocky and annoying?"

Sepia couldn't help but grin at Shadow's question. "As a matter of fact, yes it was. But there was also an air of unconcern for his well being in his voice."

Amy suddenly jumped in surprise. "Oh no, Eggman really _does_ have Sonic!" she exclaimed.

"It's about time, too," Shadow muttered.

"WHAT DID YOU SAY?!" Amy snarled.

Shadow simply shrugged. "Oh, nothing."

_**M**_

Sonic the Hedgehog was sitting down on the floor of his prison cell leaning against the wall, getting ready for another nap, when Doctor Eggman ran through his hideout's door anxiously. Sonic grinned mockingly at his captor. "No matter how often you practice, Eggman, you'll never be as fast as me," he taunted.

"Just stow that gab, hedgehog!" Eggman shouted.

"I guess the mouse has escaped from ya for good, hasn't she?" Sonic mocked, undeterred by Eggman's order. "I told ya that she was too cool to give up!"

Eggman glared at Sonic coldly. "She didn't give up, she just-" _Oh come on, how do I tell him about what had really happened earlier without looking like a scaredy-cat?_ he wondered.

The hedgehog grin grew even bigger. "You chickened out again, didn't ya?"

"I did _not_!" Eggman shouted defensively. "I just-uh-lost my cool, that's all."

"By the looks of ya, you lost your coolness a long time ago," Sonic taunted. "You're all fat and ugly, now!"

"I already told you, Sonic: it's just old age!"

"Oh, I'm sorry that I missed that little detail! Let's see, now: you're fat, ugly _and_ old. Yeah, that sounds just right!"

Eggman glared angrily at his foe. "Mock me all you want, but that won't save the mouse from her present situation."

Sonic sat up attentatively. "What do you mean?" he asked concernedly. "Where is she?"

It was Eggman's turn to grin. "She's stuck with Shadow, that's where she is," he said evilly. "Such a pity that you won't be getting out anytime soon to save her."

Much to Eggman's surprise and delight, Sonic remained quiet for the rest of the day. _Where exactly _is_ she?_ he wondered. _Is Shadow hurting or protecting her?_ These questions plagued his mind for the many remaining hours of the day and throughout the night, filling his conscience with mysterious dreams about the odd mouse.

* * *

**Please let me know what you think about this chapter.  
**


	3. Formulating the Rescue Plan

**Author's Notes:  
**

**Here's Chapter 3. This one is not as violent as the last two chapters are, but it has a little bit of humor like the second one does.**_  
_

* * *

_Sonic ran across the green hills as fast as he could, just like he always did each morning. He looked around at the houses in the area: they were oddly empty. "What the heck is going on here?" he wondered aloud. "Everyone was here last night, weren't they?"_

_"They were, Sonic," a young voice said solemnly._

_The blue hedgehog turned around to see a blonde-haired girl wearing a blue dress. "Who are you?" he asked. "What's going on?"_

_"I'm Maria," the girl replied. "Julian took everyone away at dawn, except for Shadow and Sepia."_

_"Who's Sepia?"_

_"She's the mouse that got away from Julian a few days ago. Don't worry, Shadow's taking care of her, like he did over fifty years ago on ARK. Run!" Maria suddenly shouted. "Julian's coming this way fast! Meet up with Shadow and Sepia on Angel Island. Go, now!" Maria's spirit dissolved into the air as Doctor Eggman's Egg Fleet appeared._

_Sonic turned to bolt, but a robot had just grabbed him by his legs. Three lightning bolts came seemingly from nowhere and struck the robot, causing it to explode. Sonic fell from the anihilated bot's grasp and sped off with his savior on his shoulders. "How did you do that, Sepia?" he asked breathlessly._

Sonic woke up that very moment in a sweat. _So Sepia's her name_, he thought. _But, why is she hanging out with Shadow? What was that dream trying to tell me?  
_Then the words Maria spoke hit him._ She's an old friend of Shadow's. I have to escape and meet up with them._ Without any further hesitation, he started plotting an escape plan.

_**M**_

The following morning, Vanilla invited everyone who lived near her home to a breakfast meeting. Cream had earlier pointed out to her mother that they still had an old wheelchair from a young girl named Helen who lived on Earth, suggesting that Sepia could try using it until she could walk again. Both Vanilla and Sepia were open to the idea. By the time breakfast was ready, the brown mouse had mastered the wheelchair.

Tails was still dumbstruck by the night's news. "How could Eggman have caught Sonic?" he wondered aloud. "Sonic is a lot faster than any of his robots!"

Antoine snorted. "Oui, Monsieur Tails," he said in his French accent, "but I have been telling Sonic that he's not being as careful as he should be for quite some time now."

"I doubt that you even _care_ about Sonic enough to nag him like that!" Amy exploded. "I also doubt that you have the bravery to face Eggman and his bots!"

The coyote was ashamed, but said nothing in response. He knew that Amy was right about him. He was shocked, however, when Sepia came to his defense. "Just because you're worried about Sonic doesn't mean you should yell at Antoine, Amy," Sepia said calmly. "I highly doubt that Sonic would approve of everyone losing their tempers because of his situation. It's all we can do to stay level-headed and think of the best way to help him."

Amy frowned and sighed. "I'm sorry," she apologized. "I just..." She suddenly burst into tears and sobbed, "I just can't help but worry about Sonic!"

"We all know about your obsession with the blue guy, alright?" Rouge said irritably. "Just stop your crying so we can all enjoy our breakfast!"

Shadow threw a disapproving look at the bat before looking at the pink hedgehog. "Calm down, Amy," he said as reassuringly as he could. "We'll help him out of there."

Everyone at the table, except Sepia, was shocked at Shadow's kind behavior. Amy stopped her sobbing. "You mean it, Shadow?" she choked.

"Absolutely," the black and red hedgehog replied. "Once we get a plan together, that is." He looked at his long lost friend in realization. "Do you remember the good old days in ARK when we would play 'tag' with Maria?"

Sepia stroked her abnormally furry head thoughtfully. "Not really," she replied. "Wasn't that the game where we usually distracted each other with realistic holograms of ourselves in one direction to have the others run in the opposite direction?"

"That's exactly the one I'm thinking of," Shadow said, grinning mischievously. "I think it'll come in handy when we get Sonic out of there."

"I think it will, too," the young-looking mouse said, returning the grin. "After fifty years we still have that hornery streak in us, don't we?"

Rouge piped up. "Only when he's with you, it seems. He normally doesn't act like this."

"Do you remember how to make those holograms, Sepia?" Shadow interrupted urgently.

Sepia nodded. "A little bit, yes," she responded. "Do you?"

Shadow shook his head. "No, _you_ always made them. You never let me try."

"I know how to make holograms," Tails volunteered. "They're actually very easy!"

"I'm certain that they are," Sepia told him. "If they weren't, I wouldn't have been able to make them. I'm not much of an inventor."

Bunnie Rabbot used her robotic arm to give Sepia a hearty pat on the back, almost knocking the mouse out of the wheel chair. "I reckon young Tails will be willin' to show you how it's done, sugar," she said respectfully.

Tails blushed. "Um, yeah," he said shyly. "Only if she would like me to show her."

"I'd love to know how," Sepia said politely.

The two-tailed fox blushed even more. "Uh, um, okay," he stammered.

_**M**_

Rouge had Shadow talk with her in private after breakfast. "How much _do_ you remember of your past, really?" she asked seriously.

"Everything," Shadow replied honestly.

"Oh yeah, since when?"

Shadow crossed his arms and looked at the floor. "Since the day I fought Black Doom. That was when I started having those dreams about my past, of Maria, and of Sepia." He looked up at Rouge. "On the day those soldiers raided ARK-"

"'_Raiders of the Lost Ark_'!" Tails exclaimed from outside as he and Sepia were chatting away. "_That's_ the Indiana Jones film I was thinking of. It's my favorite of the series!"

"I personally prefer '_Indiana Jones and the Last Crusade_,'" Sepia told Tails, "but '_Raiders_' is a good one too."

"Oh yeah, I forgot about '_Last Crusade_'! That one's probably my second favorite."

Rouge and Shadow waited embarrassingly for Sepia and Tails to be out of earshot before the hedgehog continued. "Anyways, on the day the soldiers raided ARK and killed Maria, I thought I could never open up to anyone again. A warmer feeling washed over me when I realized that Sepia was with me in that escape capsule. I felt that maybe Maria's memory was never going to fade away, since Sepia had been injected with Maria's blood as well as mine when she was only thirteen. Sepia inherited Maria's common sense and unconditional love, but she also got some of my powers and coloring."

"Do you know if she remembers any of that?" Rouge asked curiously.

"I doubt it," Shadow replied sadly. "She was shot in the back by a GUN soldier when she was trying to protect me a few days after we landed on Earth. I guess that having some of my blood in her allowed her to survive-and she still looks the same age after all these years because of it."

"Are you telling me that she is _ageless_? Does this make her invincible like you?"

"Yes, she is incapable of aging. But if she _were_ invincible, which would be surprising if she really _is_, I wouldn't have presumed her dead."

"But that makes no sense!" Rouge exclaimed.

"I didn't think you would get it," Shadow admitted. "I don't understand it all myself."

Sepia rolled in, accompanied by Tails, at that moment. "The holograms are finished," she told the hedgehog. "What would you like for us to do now?"

Shadow was surprised at his friend. "How did you two get finished so fast?" he demanded to know.

Tails shrugged harmlessly. "Didn't I say that holograms are easy to make?" he asked matter-of-factually.

"Okay, you got me that time," Shadow said in embarrassment. He became somewhat serious the very next moment. "Since when did you put me in charge of this operation, Sepia?"

The mouse stared into her friend's eyes sagely. "From what I learned from Eggman's rants and what Tails has told me, you know more about Eggman than the rest of us do." She grinned. "Besides, I sort of recall that you were always a take-charge sort of person."

Sepia's words caught Shadow off guard, but he masterfully hid his shock. "You and Tails go get the others and tell them to meet up here at 2 o'clock this afternoon. I'll lay out the plan then."

"Roger that, Commander," Sepia said dutifully before turning to Tails. "Help me turn this chair around and step lively now!" she said in mock severity. "Left foot first, you oaf! Left, right, left, right!"

Rouge was shocked to see Shadow smile at his friend's antics. "Don't you think she's hurting Tails's feelings?" she asked severely.

Shadow shook his head. "If she were then Tails wouldn't be grinning from ear to ear and listening to her, now would he?" he stated matter-of-factly, suppressing a chuckle.

* * *

**Author's Further Notes:**

**Yes, I am appealing to some feelings that I assume Shadow had before the GUN soldiers took over ARK and killed Maria. Well, when he and Sepia were still living on ARK that is.  
**

**Please let me know what you think about this chapter and whole story so far.  
**


	4. The Rescue (Updated)

**So here is Chapter 4-please let me know what you think about this one and the previous chapters!**

* * *

Sepia stared out of the bedroom window miserably. Shadow had ordered her to stay put while he and the others went to save Sonic. Only Vanilla, Amy, Antoine, Cream, and Cheese had remained with her.

"She'll be bored out of her mind!" Amy had argued with Shadow upon his order that Sepia stayed behind. "Do you seriously want to leave her by herself, anyway?"

"No," Shadow bluntly answered. "You, the Rabbit family and Antoine are staying here, too."

Although Amy was overly enraged that she and the mouse were being treated like children, Sepia was only a little upset that her old friend had her and the other five stay behind. Nonetheless, she did not argue and instead wished him well on the mission.

Shadow eyed Sepia suspiciously, as if he could read her thoughts. "Just stay here out of trouble, alright?" he said flatly.

The young-looking mouse nodded. "Alright, I'll do my best to refrain myself from doing otherwise. You'd better get going now if you want to be back by sundown."

"Right." Shadow turned to everyone participating. "Let's get going!" he barked.

Sepia could not help but feel as if Shadow did not trust her. _Then again,_ she thought, _he knows more about me than I remember. He hasn't told me about any of it, either. He keeps telling me that the past is the past, but I know that he's hiding something painful. Could it have something to do with..._ Sepia fought back tears of sorrow before she finished her thought. _...Maria?_

"Miss Sepia," Antoine said suddenly, interrupting Sepia's thoughts, "pardon moi, but I noteece that-a you're not feeling very well about-a something. Would you care to tell moi?"

"It's nothing, Antoine," Sepia said shyly, embarrassed that she had revealed her emotions to the coyote. "But thank you for your concern."

"You're welcome," Antoine said shyly. "Would you like-a some earl grey tea? Madame Vanilla just made a fresh pot-a of it."

"Um, maybe later," Sepia answered. _Wow, this is awkward,_ she thought.

"Oh, a-alright-a." _Wow, this is very maladroit,_ Antoine thought.

Sepia suddenly gasped in surprise. "What's the matter?" Antoine asked concernedly.

The eternally young mouse pointed out the window. "What is that big green rock?" she said in a startled tone. "I've never seen it before."

Antoine was just as startled as his new friend was. "The Master Emerald!" he exclaimed. "It's supposed to be on Angel Island, not floating around out here!"

"It's not just floating around," Sepia stated after a moment of closely examining the scene. "Eggman's taking it! He's heading back to his fort where the others are going!" She spun her chair out of the room impulsively. "Stay here and protect everyone, Antoine!" she called behind her. "I'll be back in a little while, I promise!" _So much for refraining myself_, she thought grimly.

_**M**_

"That oaf Knuckles should have figured that I'd pay his place a visit," Doctor Eggman chuckled to himself. "It's a good thing for him that he was on vacation- -I would've used my new paralysis device on him and taken him with me, ha ha ha!"

Eggman stopped when he saw a sight that froze the blood in his veins. All of the creatures living on the land, except for Sonic, were charging at his fort. His robot sentries were fighting them off to the best of their abilities, but the robots were easily overwhelmed. "Do I have to do _everything_ myself?" Eggman muttered, speeding to his fort in his hovercraft with all guns blazing.

Sepia rode over the rolling hills in her wheelchair as fast as she could. _I'm sorry I'm disobeying, Shadow,_ she thought. _But I have to try to slow Eggman down before he has the chance to take _you_ prisoner._

Eggman's hovercraft got in Sepia's path at that moment. The mouse gasped in surprise as the doctor's large hand enveloped itself around her and brought her up to his face.

"What do we have here?" he mocked. "It looks like I can bring an end to the rodent infestation after all!"

The mouse kicked herself out of the villain's grasp, falling into the hovercraft. She immediately turned the vehicle's steering wheel in the opposite direction of Eggman's fort. Eggman regained control of the hovercraft after he shocked Sepia with his paralyzing taser, leaving her incapacitated as he tightly bound a thick rope around her paws. She was about to shout in warning to her friends, but her captor covered her mouth with his hand immediately.

"You put up a good fight, mouse," Eggman taunted his prisoner, "but you're completely helpless without that hedgehog friend of yours."

_**M**_

Shadow, unaware of Sepia's predicament, motioned to his followers hastily. "We go now!" he whispered urgently. "You all know the plan!"

Tails flew into the fort's computer room, where television screens revealed what each camera was viewing in each room. He was shocked to see a camera was looking up random YouTube videos ranging from old to new television shows, classical to heavy metal music, and even shoot-em-up dramas to parodies. _Whoa,_ Tails thought, _it's no wonder that Eggman's so fat- -he's too entertained to get up from this chair!_

Bunnie Rabbot tore down every door that stood in her path with her bionic arm. Rouge glided through the hallways, looking for the cell Sonic was in. Shadow kept disappearing and reappearing in different rooms of the fort until he came across an all-too familiar room: _the prison_. A blue figure leaned lazily against the wall of the farthest cell.

"Hey, wake up Faker!" Shadow barked.

The blue creature looked at Shadow with a start. "My name is _Sonic_ like I've told you a million times before, Phony!" he shot back.

"Hey, it's not _my_ fault everyone mistook me for you just because I'm a hedgehog!" Shadow snarled.

"Quit your bickering, sugar-hogs!" Bunnie ordered as she entered the room. "We're here for a reason, remember?"

"A reason that is now in vain!"

Bunnie, Shadow and Sonic spun around in surprise to see Doctor Eggman standing on the opposite side of the prison, holding a struggling Sepia hostage with a hand clamped over her mouth. "Shadow!" Tails's voice crackled through the walkie-talkie in Shadow's belt. "Get out of there! Eggman's back!"

"You're a little too late, Tails!" Shadow shouted into the radio. "What kept you from not noticing until now, anyway?"

"Um," Tails stuttered, thinking about the parody video on YouTube he had just seen depicting a rabbit named Hazel from the film _Watership Down _lip-synching the Onision song "I'm a Banana." "Well, it went like this- -"

Shadow rolled his eyes impatiently. "Tell me later!" he interrupted. His eyes shifted to his helpless friend before he glared dangerously at Eggman. "Let her go," he growled.

Eggman laughed uproariously. "And what makes you think that I will?" he asked curiously.

"The realization that you have the hologram version of her," Shadow returned with a sly grin.

"You're lying to me, aren't you?"

"No, Doctor. Didn't you see everyone charging at your fort?"

"Yeah, that's why I grabbed the mouse and came in here the back way."

"They were all holograms," Shadow continued, his grin growing bigger and creepier. "You're holding a hologram of her hostage, you idiot!"

Eggman released Sepia angrily, allowing her to fall to the floor. "Oh, fine!" he shouted. "Take the stupid hologram and get into that cell with Sonic!"

Sepia jumped to her feet and kicked Eggman against the nearest wall. "Over my dead body, round-waist!" she yelled.

The doctor lunged forward and tightly gripped Sepia's shirt collar. "You'll pay for that, mouse!" he barked.

Bunnie ripped the door to Sonic's cell off of its hinges with one swipe of her robotic arm. "Come on, sugars!" she drawled urgently.

Sonic grabbed Bunnie before dashing out of the prison block. Shadow swiftly snatched Sepia away from Eggman and sped after Sonic. Rouge and Tails flew through the back door just moments prior to their companions' escape.

Eggman knew he was unable to do anything for the moment. "You pesky rodents!" he cursed. "You will pay soon, do you hear me? You _will_ pay!"

_**M**_

"What were you thinking back there, Sepia?" Shadow snapped once the rescue party returned to the village. "You put all of our lives in jeopardy! I told you to stay here!"

"I'm sorry, but Eggman would have found you sooner if not for me," Sepia countered as Antoine untied the rope that was bound around her paws. "I saw him heading back to the fort with the Master Emerald. I had to do something!"

"How do I know that I can trust your word?" the hedgehog snarled. "You're too unpredictable for your own good anyway, you know that? Get out of my sight, now!"

Antoine came to his friend's defense. "I saw Robotnik with the Emerald, as well-a," he stated honestly. "Sepia told moi to stay here while she tried to stoppa him."

"Shut up and sit down, Antoine!" Shadow yelled.

"You foirst, Shadow!" Antoine shot back, surprising everyone and himself at his sudden boldness.

Sepia stared into Shadow's eyes harshly. "You knew that I would disobey before I even did," she stated angrily. "How is that called 'unpredictable?'"

Shadow glared at her. "Save it for tomorrow."

"No, _now_!" Sepia snapped.

The black hedgehog and everyone witness gasped in surprise at Sepia's outburst. "I'm serious, Shadow!" the mouse continued. "I need to know more about my past, no matter how painful it is, so I won't make the same mistakes. I should _not_ have to learn the hard way all over again, don't you agree?"

After a moment of silence, Shadow finally gave in with a sigh and a slow nod of the head. "Alright, I'll tell you everything..."

* * *

**Yes, now some strain in Shadow and Sepia's relationship is depicted. Did I do good with it, or do I need to work on it a little bit? Also, I had done some strange spelling with Antoine's lines to express his French accent. The word **_**maladroit**_** is French for **_**awkward**_**.**


	5. Sepia's Past

**Author's Notes:**

**Here's Chapter 5. This one mentions the tragic moments of our heroine's past and may make you cry, although it will help you better understand the story.  
**

* * *

"You mean, I was _also_ an experiment?" Sepia asked in an astonished voice.

Shadow nodded sagely. "That's exactly what I mean," he replied. "Professor Gerald wanted to know that my DNA would fight off NIDS. It did, but the side effects that occurred were unwanted."

"What side effects?"

"My blood gave you the power of Chaos Lightning, and caused you to have that black fur on your head. Not only that, but you became more than a laboratory mouse: you became a creature that could walk on two legs, talk like humans, and be a weapon if used as such." The hedgehog paused and looked away sadly. "The main reason why the GUN soldiers invaded our home was to capture us two. They thought that we would be major threats to the human race, but that never would have happened-" his eyes filled with angry tears- "if they had not killed Maria!"

Sepia had Shadow look into her eyes. "You-you sought revenge, didn't you?" she asked, trying hard to make her voice sound non-accusing.

"Yes," Shadow replied in a troubled whisper.

The mouse was struck hard by a sudden realization. _I knew this would happen_, she thought. _I've known all this time, ever since that day on ARK when I heard the professor talking to Black Doom about Shadow. Wait a minute, Black Doom?_ "I-I've been keeping a secret too, Shadow," Sepia told him.

"What do you mean?" Shadow asked in astonishment. "I've never known you to lie."

"I'm ashamed that you've killed many people, but I can't say that I'm surprised," the mouse replied ashamedly. "I once heard Gerald talking to a nasty creature called Black Doom. Black Doom kept saying that he expected to see 'better' results with the use of his DNA to make you, meaning that he had not wanted to see you love anyone. I could sense a mix of good _and_ bad in you, but there's a bit of bad in everyone."

Shadow looked at his friend suspiciously. "When did you learn about this?"

Sepia thought hard for a moment, muttering: "I'm not sure..." Her eyes went wide. "It was the same day I was rescued from Earth, just a week after you were created. It was about an hour after we played tag with Maria when I heard the conversation from a nearby broom closet."

Rouge looked at Sepia in astonishment. "You remember it _that_ clearly?"

"Yeah," Sepia said sadly, a tear falling from her left eye. "I remember everything now. I'm sorry, Shadow."

The black hedgehog wiped away Sepia's tear with a finger. "Don't worry about it, kid," he said reassuringly. "I'm sorry I refused to tell you anything sooner. Do you recall what happened before you were rescued by ARK?"

The mouse nodded as more tears streamed down her cheeks. "My entire family was taught to be a warrior," she choked. "The humans came with poison and bombs one day. My parents tried to fight off the humans to keep them away from me, but they were killed almost instantly. The murderers almost got me too when Black Doom scared them off. He took me up to ARK, going on and on about how disgusting he thought of humans to be. I soon agreed with him when I was strapped down by Gerald and injected with two different kinds of DNA- -yours and Maria's. My own DNA painfully mixed with both kinds, making me what I am now- -a child of two brave mice, and the part-sibling of a powerful hedgehog and a loving girl."

"I never knew of Black Doom to save a life," Shadow stated, hugging Sepia comfortingly as she softly cried. He tried to ignore everyone's shock at his sudden softness towards another creature. "Then again, I only knew of him to kill every living thing in his path."

"Maybe he _was_ good at first," Cream suggested, fighting back her own tears. "What if humans killed his family like they had Sepia's and he felt sorry for her?"

"Chao chao," Cheese agreed in a sad tone.

"That's exactly what happened," Sepia said sadly. "Doom was speaking to me while I was recovering from operation and getting used to the new blood, explaining why he didn't leave me on Earth to die. He said that my family functioned and was eliminated the same way his was. He blamed the entire human race for taking away what he cherished most. He didn't want you to love because he felt that if he could no longer love, neither should any of his children."

"May I change the subject here?" Sonic asked pleadingly.

Sepia nodded. "Yes, please do. What's on your mind?"

"Eggman's still after us," he said energetically. "We need to set up our defenses tonight."

"It's not-a like you to be pan-eeked about it," Antoine said observantly, "but you make a good point-a."

Sonic grinned at the coyote. "It's not like you to agree with me about these issues or anything at all, Antoine," he replied.

"Well, we've got the cowardly coyote and the obnoxious hedgehog both talking about defending our land," Rouge said humorously. "What's next? The knuckle-headed echidna agreeing with the idea of learning to do the hula?"

"Hey guys, you should really consider taking a trip to Hawaii! It's a life-changing experience!"

All creatures spun around to see a red echidna (whom Sepia correctly presumed to be Knuckles) standing in the doorway. He was wearing a green hula skirt and a brightly colored flower lei, causing the onlookers to either gag, giggle or burst into spontaneous laughter. Rouge covered her eyes with her right hand in embarrassment. "I should've kept my mouth shut," she muttered.

Knuckles tore off his apparel at that moment. He finally noticed Sepia for the first time. "Did I miss out on something while I was gone?" he asked.

Sepia politely introduced herself to Knuckles before she explained the past few days' events. "That freak will pay for this," the echidna muttered darkly when the mouse had finished. "I'll get the Master Emerald back from him, I swear it!"

"I don't doubt it," Sepia told him.

_**M**_

Eggman sat at his desk irritably, struggling to come up with a strategic battle plan against the villagers. He looked up at a picture that hung up on his wall, which was a large copy of a photograph of Professor Gerald Robotnik and Maria Robotnik. "You were the greatest scientist to ever live, Grandfather," he murmured to his long-lost family member. "You created the Ultimate Life-form and part of the mouse, who are now against me. How do I deal with this problem?"

_"Give up your evil ways, Julian,"_ Gerald's voice echoed through his grandson's mind. _"Only then will you be rid of your problem!"_

"Being good is no fun!" Eggman protested.

_"You've never given it a try, now have you?"_

"And I don't plan to! Ah, who needs _your_ help anyway? My IQ is greater than yours ever was!" Eggman focused back on his evil plot. "Let me see here... Ah-ha! Now _that's_ what I'll do. I'll position some of my robots here..."

* * *

**That's it for Chapter 5. Let me know what you think about it and the whole story so far. Please don't hate me for what I suggested was Black Doom's reason for hating humans: I found it more believable than hating humans for being lesser creatures!  
**

**Yeah, this chapter was definitely the most emotional one I've written for this story. That's why I decided to add in the scene with Knuckles wearing the hula skirt: I felt that I _had_ to throw in some comic relief, even if it was at least a little random.**

**Also: I'm out of ideas for this story for the time being, but I'm also working on a crossover of Lethal Weapon and Watership Down called _Lethal Rabbit_ (although it is now a side-project) as well as a _Lion King_ story and one of _Redwall_. I've also been writing some Batman Beyond stories, two of which are already finished and the third one is in progress, even though I haven't posted any of that one yet. Oh yeah: there's also a parody of _Batman_ that I wrote on Christmas Day of 2012 (although it was posted then, it does not contain any holiday themes). Check those out if you'd like to!  
**


	6. Sepia's Nightmare

**Author's Notes:**

**Here's Chapter 6. More serious than the last few, but here it is anyway. Let me know what you think!**

* * *

_Sepia heard Amy, Tails, and Cream scream in terror from the other side of the hill. Eggman cackled evilly as he sped away in his hovercraft. It was then that Sepia saw that the three troubled creatures were held prisoner in a net that was in the backseat of the hovercraft. The eternally young mouse gave a mighty leap at the villain's hovercraft, grabbing hold of the back of it. _

_A net suddenly shot out from below and wrapped itself around Sepia. She fell to the ground ten feet below, landing with a loud and painful thud. A robot ran from the other side of the hill to where Sepia had fallen and pointed a gun at her face. All Sepia could do was lay where she was helplessly and wait for the robot to pull the trigger-_

_-or wait for a miracle to happen._

_The robot suddenly exploded, dropping the gun at that moment. Sepia instinctively covered her face as shrapnel was launched everywhere. She uncovered her face in time to see Shadow free her of the net, which was now cut by the metal pieces. "Thanks, Shadow," Sepia said to him respectfully._

_Shadow pulled his friend up to her feet as more robots charged in their direction with all of the other villagers in nets. A robot stopped with a net-launcher aimed directly at the two creatures. A flash of blue pulled them out of the net's path and dashed up the nearby cliff with seemingly endless energy. They stopped a few yards away from the cliff's edge._

_"Are you guys alright?" the blue rescuer asked._

_"Yeah, thanks Sonic," Sepia gasped._

_"We'd better get moving," Shadow said urgently. "Eggman might circle back after us- ungh!"_

_Two gunshots echoed through the nearby trees, striking Shadow and Sonic each in the chest one at a time. They fell to the ground in lifeless heaps. "_NO!_" Sepia screamed in dismay._

_Eggman walked towards Sepia, holding a pistol that had smoke fuming from the barrel. "Oh yes, runt," he said evilly. "No one is here to save you, now!" He lifted his small gun up, aimed it at the mouse, and squeezed the trigger all the way, letting out a loud bang. Sepia felt a sharp pain in her chest momentarily.  
_

_**M**_

Sepia let out a terrified scream as her eyes snapped open. A spider had landed on her chest and had bitten her in the center of it. Overwhelmed by her anxiety, she began to weep uncontrollably. Shadow- who had been sleeping in a chair that was next to Sepia's bed- awoke to her shout. He knelt down next to the bed and gently hugged her. "I-it seemed s-so real, Shadow," Sepia stammered. "Shh, it's alright kid," he said reassuringly. "It was just a nightmare. Sonic and I are still alive, and no one is captured."

The mouse looked at her friend with teary eyes in surprise. "How did you know about my nightmare?" she choked.

"I had the same one myself just now," Shadow replied softly. "Try to get some more sleep."

"It's still nighttime?"

"Yeah, it's about one-thirty in the morning."

"Oh. Well, I'll give it a try."

"Alright. Goodnight, Sepia."

"Goodnight, Shadow."

Sepia dozed off momentarily, allowing Shadow to return to his spot in the chair. _I already knew that we had the same nightmare_, he wondered, _but what's going on? Is there something that concerns us both- and Sonic?_ These thoughts filled his mind as he fell to sleep once more, unaware that several of Eggman's robots were lurking around just outside of the house.

* * *

**Yes, this was a very short chapter. The next one will be longer and will clear up the mysteries surrounding this chapter: Why did Shadow and Sepia get the same dream as each other? Did Sonic have it as well? What exactly is Eggman up to? More importantly, why did the chicken cross the road? Okay, it's not _so_ important, but- who knows?- it might have something to do with this story later.**

* * *

**I will be having this story and _Lethal Rabbit_ on hold until I get more reviews for both of them.  
**


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